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jianyangqt / gcta

GCTA software
GNU General Public License v3.0
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phenotype file not found in fastGWA #55

Closed Wenxi-Zhang closed 10 months ago

Wenxi-Zhang commented 10 months ago

Hello,

In the fastGWA example, my command: ./gcta-1.94.1 --grm-sparse test_sp_grm --fastGWA-mlm --pheno test.phen --out geno_assoc which modified from this command:

image

I got this: --grm-sparse test_sp_grm --fastGWA-mlm --pheno test.phen --thread-num 10 --out geno_assoc The program will be running with up to 10 threads. Error: no phenotype file found.

Under the current directory I have a phenotype file named “test.phen”. When I tried this command: gcta64 --grm test --pheno test.phen --reml --out test --thread-num 10 in estimating the variances, “--pheno test.phen” works.

How can I deal with this issue?

longmanz commented 10 months ago

Hi, You need to input the genotype file using either "--bfile" or "--mbfile". But it is true the error message seems to be mis-leading here. Thank you for reporting this. We will fix it.